I have been having this issue for several months now and have not found a solution that works.
Multi-Media_Server
Version: 7.2.9-13
Videos: 2867Songs: 8142Photos: 0
I create all the shares in Twonky 16 folders in a 2nd (attached (Elements_107C-1)) HDD and 13 in the root of the WD drive.
One of the root folders is TV_Shows that has 7 sub-folders under it and these are always remembered, the folders in the 2nd drive are always remembered too. BUT I have to constantly reset the 14 root folders with videos (movies) in them.
What am I doing wrong that Twonky will no remember these root folders?

What changed a couple of weeks ago? Did you change anything on the local network? Did you change anything on the My Cloud (like update the firmware)? Are you using a brand new computer or other device to access the My Cloud? What program or software are you using to access the Twonky DLNA media server?